Package Bio :: Package expressions :: Package swissprot :: Module ipi
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Module ipi

source code

Expression for IPI format.

IPI is nearly swissprot, but contains some differents which makes the Swissprot parsers choke.

Variables [hide private]
  ID_exp = Martel.Group("ID", Martel.Str("ID ")+ Std.dbid(Mart...
  DT_created_exp = Martel.Str("DT ")+ Time.make_expression("%(...
  DT_seq_update_exp = Martel.Str("DT ")+ Time.make_expression(...
  DT_ann_update_exp = Martel.Str("DT ")+ Time.make_expression(...
  replacements = [("ID", ID_exp), ("DT_created", DT_created_exp)...
  record = Martel.replace_groups(sprot40.record, replacements)
  format_expression = Martel.replace_groups(sprot40.format_expre...
  format = Martel.replace_groups(sprot40.format, replacements)
  __warningregistry__ = {('Bio.expressions was deprecated, as it...
Variables Details [hide private]

ID_exp

Value:
Martel.Group("ID", Martel.Str("ID   ")+ Std.dbid(Martel.Group("entry_n\
ame", Martel.Re("[\w.]+")), {"type": "primary", "dbname": "sp"})+ Mart\
el.Spaces()+ Martel.Word("data_class_table")+ Martel.Str(";")+ Martel.\
Spaces()+ Martel.Word("molecule_type")+ Martel.Str(";")+ Martel.Spaces\
()+ Martel.Digits("sequence_length")+ Martel.Str(" AA.")+ Martel.AnyEo\
l())

DT_created_exp

Value:
Martel.Str("DT   ")+ Time.make_expression("%(DD)-%(Jan)-%(YYYY)")+ Mar\
tel.Str(" (IPI Human rel. ")+ Martel.Float("release")+ Martel.Str(", C\
reated)")+ Martel.AnyEol()

DT_seq_update_exp

Value:
Martel.Str("DT   ")+ Time.make_expression("%(DD)-%(Jan)-%(YYYY)")+ Mar\
tel.Str(" (IPI Human rel. ")+ Martel.Float("release")+ Martel.Str(", L\
ast sequence update)")+ Martel.AnyEol()

DT_ann_update_exp

Value:
Martel.Str("DT   ")+ Time.make_expression("%(DD)-%(Jan)-%(YYYY)")+ Mar\
tel.Str(" (IPI Human rel. ")+ Martel.Float("release")+ Martel.Str(", L\
ast annotation update)")+ Martel.AnyEol()

replacements

Value:
[("ID", ID_exp), ("DT_created", DT_created_exp), ("DT_seq_update", DT_\
seq_update_exp), ("DT_ann_update", Martel.Opt(DT_ann_update_exp))]

format_expression

Value:
Martel.replace_groups(sprot40.format_expression, replacements)

__warningregistry__

Value:
{('Bio.expressions was deprecated, as it does not work with recent ver\
sions of mxTextTools. If you want to continue to use this module, plea\
se get in contact with the Biopython developers at biopython-dev@biopy\
thon.org to avoid permanent removal of this module from Biopython',
  <type 'exceptions.DeprecationWarning'>,
  8): 1}